Without more details I can only guess at what is going wrong. The
script in question is a cpptraj script, not ptraj - are you using
cpptraj, and if so what version of cpptraj are you using? In the
output of cpptraj does it state it is setting up any solvent
donors/acceptors? Are the water residues in your system named WAT?
-Dan
On Mon, Jun 27, 2016 at 10:35 PM, chemjxn <chemjxn.126.com> wrote:
> Dear Sir,
>
>
> I use AMBER14 to MD simulation, and then analyse the result. when analysing hydrogen bond, I use the ptraj script named "cpptraj.hbond.in" that is gained in the website http://www.amber.utah.edu/AMBER-workshop/London-2015/Hbond/. Note that the protein/ligand complex I investigate include water molecule. However, I found the hydrogen bonds formed by residue and water is not included in the result. I donot know how to do. Please help me. THANK YOU VERY MUCH! Looking forward to your reply.
>
>
> Sincerely,
> Liyan
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Jun 28 2016 - 06:00:02 PDT
